Merge pull request #169 from khanlab/Docs-updates

Updates to Docs with environment management tips

docs/contributing/contributing.md

@@ -127,3 +127,10 @@ multiple subjects in each job), 1 32core job for N subjects (e.g. 10):
 
     hippunfold PATH_TO_BIDS_DIR PATH_TO_OUTPUT_DIR participant \
     --profile cc-slurm --group-components subj=10
+
+## Environment management
+By default, singularity stores images in your home directory. HippUnfold also stores several files similarly. If your home directory is full or otherwise inaccessible, you may want to change this with the following commands:
+
+    export SINGULARITY_CACHEDIR=/YOURDIR/.cache/singularity
+    export SINGULARITY_BINDPATH=/YOURDIR:/YOURDIR
+    export HIPPUNFOLD_CACHE_DIR=/YOURDIR/.cache/hippunfold/

docs/getting_started/installation.md

@@ -73,4 +73,9 @@ Run it with maximum number of cores:
     singularity run -e khanlab_hippunfold_latest.sif \
     PATH_TO_BIDS_DIR PATH_TO_OUTPUT_DIR participant -p --cores all
 
-Note that you may need to adjust your [Singularity options](https://sylabs.io/guides/3.1/user-guide/cli/singularity_run.html) to ensure this container can read and write to yout input and output directories, repsectively. 
+Note that you may need to adjust your [Singularity options](https://sylabs.io/guides/3.1/user-guide/cli/singularity_run.html) to ensure this container can read and write to yout input and output directories, repsectively. For example, if your home directory is full or inaccessible, you may wish to set the following singularity parameters:
+
+    export SINGULARITY_CACHEDIR=/YOURDIR/.cache/singularity
+    export SINGULARITY_BINDPATH=/YOURDIR:/YOURDIR
+
+, where `YOURDIR` is your preferred storage location.